Can someone explain exactly how zero-joints works - I still get 'random' errors....

How are you meant to use zero joints?

Do you have to animate all in one go?

I don't, what I do is activate zero joints - animate one thing... save, reopen - activate zero joints - animate another thing...

Do I need to do zj every time I reopen a model?

Sometimes I get errors sometimes I don't... It doesn't seem logical

What sort of errors? You shouldn't have to either animate all in one go or run it everytime you start a new session. Make sure that you're not in animation mode when you run zero joints. If you modify the positions of the bones after you've started animating, it seems to mess things up sometimes.

an example:

I'll do zero joints, animate running, export, save, exit -- everything's fine

then i'll reopen, do zero joints, animate standing, export, ---- and his stand has gone all chaotic, limbs flailing about etc.

sometimes there's no problem